Selection versus demography: A multilocus investigation of the domestication process in maize

Molecular Biology and Evolution

Volumn 21, Issue 7, 2004, Pages 1214-1225

  Tenaillon, Maud I ^a,b   U'Ren, Jana ^b   Tenaillon, Olivier ^c   Gaut, Brandon S ^b  

^a INRA Institut National de la Recherche Agronomique   (France)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c INSERM   (France)

Author keywords

Bottleneck; Coalescence; Nucleotide diversity; Recombination

Indexed keywords

NUCLEOTIDE;

AGRONOMIC TRAIT; ARTICLE; BOTTLENECK POPULATION; CHROMOSOME 1; D8 GENE; DEMOGRAPHY; DOMESTICATION; GENE; GENE LOCUS; GENETIC SELECTION; GENETIC VARIABILITY; MAIZE; NONHUMAN; NUCLEOTIDE SEQUENCE; POPULATION SIZE; SEQUENCE ANALYSIS; SIMULATION; STATISTICS; TB1 GENE; TS2 GENE; ZAGL1 GENE;

AMINO ACID SEQUENCE; BASE SEQUENCE; DEMOGRAPHY; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; RECOMBINATION, GENETIC; SELECTION (GENETICS); VARIATION (GENETICS); ZEA MAYS;

ZEA; ZEA MAYS;

EID: 3042595170     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msh102     Document Type: Article

References (65)

1. Andolfatto, P., and M. Przeworski. 2001. Regions of lower crossing over harbor more rare variants in African populations of Drosophila melanogaster. Genetics 158:657-665.
2. Begun, D. J., and C. F. Aquadro. 1992. Levels of naturally occurring DNA polymorphism correlate with recombination rates in Drosophila melanogaster. Nature 356:519-520.
3. Begun, D. J., and P. Whitley. 2000. Reduced X-linked nucleotide polymorphism in Drosophila simulans. Proc. Natl. Acad. Sci., U.S.A. 97:5960-5965.
4. Charlesworth, B. 1994. The effect of background selection against deleterious mutations on weakly selected, linked variants. Genet. Res. 63:213-227.
5. Clark, R.M., E. Linton, J. Messing, and J. Doebley. in press. Patterns of diversity in the genomic region near the maize domestication gene, tb1. Proc. Natl. Acad. Sci., U.S.A.
6. Davis, G. L., M. D. McMullen, C. Baysdorfer et al. (13 coauthors). 1999. A maize map standard with sequenced core markers, grass genome reference points and 932 expressed sequence tagged sites (ESTs) in a 1736-locus map. Genetics 152:1137-1172.
7. Depaulis, F., S. Mousset, and M. Veuille. 2003. Power of neutrality tests to detect bottlenecks and hitchhiking. J Mol Biol Evol. 57:Supl 1:S190-S200.
8. Doebley, J., A. Stec, and L. Hubbard. 1997. The evolution of apical dominance in maize. Nature 386:485-488.
9. Doebley, J., A. Stec, and C. Gustus. 1995. Teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance. Genetics 141:333-346.
10. Dvorak, J., M.-C. Luo, and Z.-L. Yang. 1998. Restriction fragment length polymorphism and divergence in the genomic regions of high and low recombination in self-fertilizing and cross-fertilizing Aegilops species. Genetics 148:423-434.
11. Ewens, W. J. 1972. The sampling theory of selectively neutral alleles. Theoretical Population Biology 3:87-112.
12. Eyre-Walker, A., R. L. Gaut, H. Hilton, D. L. Feldman, and B. S. Gaut. 1998. Investigation of the bottleneck leading to the domestication of maize. Proc. Natl. Acad. Sci., U.S.A. 95:4441-4446.
13. Fearnhead, P., and P. Donnelly. 2001. Estimating recombination from population genetic data. Genetics 159:1299-1318.
14. Fu, Y.-X., and W.-H. Li. 1993. Statistical tests of neutrality of mutations. Genetics 133:693-709.
15. Gaut, B. S., and M. T. Clegg. 1993. Molecular evolution of the Adhl locus in the genus Zea. Proc. Natl. Acad. Sci. U.S.A. 90:5095-5099.
16. Gaut, B. S., and A. D. Long. 2003. The lowdown on linkage disequilibrium. Plant Cell 15:1502-1506.
17. Gaut, B. S., B. R. Morton, B. M. McCaig, and M. T. Clegg. 1996. Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc. Natl. Acad. U.S.A. 93:10274-10279.
18. Hall, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucl. Acids Symp. Ser. 41:95-98.
19. Hanson, M. A., B. S. Gaut, A. O. Stec, S. I. Fuerstenberg, M. M. Goodman, E. H. Coe, and J. Doebley. 1996. Evolution of anthocyanin biosynthesis in maize kernels: the role of regulatory and enzymatic loci. Genetics 143:1395-1407.
20. Harberd, N. P., and M. Freeling. 1989. Genetics of dominant gibberellin-insensitive dwarfism in maize. Genetics 121:827-838.
21. Hellmann, I., I. Ebersberger, S. E. Ptak, S. Paabo, and M. Przeworski. 2003. A neutral explanation for the correlation of diversity with recombination rates in humans. Am. J. Hum. Genet. 72:1527-1535.
22. Hilton, H., and B. S. Gaut. 1998a. Speciation and Domestication in maize and its wild relatives: evidence from the Globulin-1 gene. Genetics 150:863-872.
23. Hilton, H., and B. S. Gaut. 1998b. Speciation and domestication in maize and its wild relatives: Evidence from the globulin-1 gene. Genetics 150:863-872.
24. Hudson, R. R. 1987. Estimating the recombination parameter of a finite population model without selection. Genet. Res. Camb. 50:245-250.
25. Hudson, R. R. 2001. Two-locus sampling distributions and their application. Genetics 159:1805-1817.
26. Hudson, R. R., and N. L. Kaplan. 1995. Deleterious background selection with recombination. Genetics 141:1605-1617.
27. Hudson, R. R., M. Kreitman, and M. Aguadé. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116:153-159.
28. Iltis, H. H. 1983. From teosinte to maize: the catastrophic sexual transmutation. Science 222:886-894.
29. Irish, E. E., J. A. Langdale, and T. M. Nelson. 1994. Interactions between tassel seed genes and other sex determining genes in maize. Dev. Genet. 15:155-171.
30. Irish, E. E., and T. M. Nelson. 1993. Development of tassel seed 2 inflorescences in maize. Am. J Bot. 80:292-299.
31. Kaplan, N. L., R. R. Hudson, and C. H. Langley. 1989. The "Hitchiking Effect" revisited. Genetics 123:887-899.
32. Kraft, T., T. Sall, I. MagnussonRading, N. O. Nilsson, and C. Hallden. 1998. Positive correlation between recombination rates and levels of genetic variation in natural populations of sea beet (Beta vulgaris subsp. maritima). Genetics 150:1239-1244.
33. Lercher, M. J., and L. D. Hurst. 2002. Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet. 18:337-340.
34. Long, A., B. F. Benz, D. J. Donahue, A. J. T. Jull, and T. J. Toolin. 1980. First Direct AMS Dates on Early Maize from Tehuacan, Mexico. Radiocarbon 31:1035-1040.
35. Lukens, L. N., and J. Doebley. 1999. Epistatic and environmental interactions for quantitative trait loci involved in maize evolution. Genetical Research 74:291-302.
36. Marais, G., D. Mouchiroud, and L. Duret. 2003. Neutral effect of recombination on base composition in Drosophila. Genet. Res. 81:79-87.
37. Matsuoka, Y., Y. Vigouroux, M. M. Goodman, J. Sanchez G., E. Buckler, and J. Doebley. 2002. A single domestication for maize shown by multilocus microsatellite genotyping. Proc. Natl. Acad. Sci. U.S.A. 99:6080-6084.
38. Maynard-Smith, J., and J. Haigh. 1974. The hitch-hiking effect of a favorable gene. Genet. Res. 23:23-35.
39. McDonald, J. H., and M. Kreitman. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-654.
40. Nachman, M. W. 1997. Patterns of DNA variability at X-linked loci in Mus domesticus. Genetics 147:1303-1316.
41. Nachman, M. W., V. L. Bauer, S. L. Crowell, and C. F. Aquadro. 1998. DNA variability and recombination rates at X-linked loci in humans. Genetics 150:1133-1141.
42. Payseur, B. A., and M. W. Nachman. 2002. Natural selection at linked sites in humans. Gene 300:31-42.
43. Piperno, D. R., and K. V. Flannery. 2001. The earliest archaeological maize (Zea mays L.) from highland Mexico: new accelerator mass spectrometry dates and their implications. Proc. Natl. Acad. Sci. U.S.A. 98:2101-2103.
44. Pluzhnikov, A., A. Di Rienzo, and R. R. Hudson. 2002. Inferences about human demography based on multilocus analyses of non coding sequences. Genetics 161:1209-1218.
45. Przeworski, M. 2002. The signature of positive selection at randomly chosen loci. Genetics 160:1179-1189.
46. Reich, D. E., M. Cargill, S. Bolk, J. Ireland, P. C. Sabeti, D. J. Richter, T. Lavery, R. Kouyoumjian, S. F. Farhadian, R. Ward, and E. S. Lander. 2001. Linkage disequilibrium in the human genome. Nature 411:199-204.
47. Remington, D. L., J. M. Thornsberry, Y. Matsuoka, L. M. Wilson, S. R. Whitt, J. Doebley, S. Kresovich, M. M. Goodman, and E. S. Buckler. 2001. Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc. Natl. Acad. Sci. U.S.A. 98:11479-11484.
48. Rozas, J., and R. Rozas. 1999. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174-175.
49. Smith, B. D. 1998. The emergence of agriculture. W. H. Freeman, New York.
50. Stephan, W., and C. H. Langley. 1998. DNA polymorphism in Lycopersicon and crossing-over per physical length. Genetics 150:1585-1593.
51. Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
52. Tajima, F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437-460.
53. Tenaillon, M. I., M. C. Sawkins, L. K. Anderson, S. M. Stack, J. Doebley, and B. S. Gaut. 2002. Patterns of diversity and recombination along chromosome 1 of maize (Zea mays ssp. mays L.). Genetics 162:1401-1413.
54. Tenaillon, M. I., M. C. Sawkins, A. D. Long, R. L. Gaut, J. F. Doebley, and B. S. Gaut. 2001. Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp mays L.). Proc. Natl. Acad. Sci. U.S.A. 98:9161-9166.
55. Thornsberry, J. M., M. M. Goodman, J. Doebley, S. Kresovich, D. Nielsen, and E. S. Buckler. 2001. Dwarf8 polymorphisms associate with variation in flowering time. Nat. Genet. 28:286-289.
56. Vigouroux, Y., J. S. Jaqueth, Y. Matsuoka, O. S. Smith, W. D. Beavis, J. S. C. Smith, and J. Doebley. 2002a. Rate and pattern of mutation at microstaellite loci in maize. Molecular Biology and Evolution 19:1251-1260.
57. Vigouroux, Y., M. McMullen, C. T. Hittinger, K. Houchins, L. Schulz, S. Kresovich, Y. Matsuoka, and J. Doebley. 2002b. Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proc. Natl. Acad. Sci. U.S.A. 99:9650-9655.
58. Wall, J. D. 2000. A comparison of estimators of the population recombination rate. Mol. Biol. Evol 17:156-163.
59. Wang, R. L., A. Stec, J. Hey, L. Lukens, and J. Doebley. 1999. The limits of selection during maize domestication. Nature 398:236-239.
60. Watterson, G. A. 1975. On the number of segregating sites in genetical models withough recombination. Theor. Popul. Biol. 7:188-193.
61. Weiss, G., and A. von Haeseler. 1998. Inference of population history using a likelihood approach. Genetics 149:1539-1546.
62. White, S. E., and F. D. Doebley. 1999. The molecular evolution of terminal earl, a regulatory gene in the genus Zea. Genetics 153:1455-1462.
63. Whitt, S. R., L. M. Wilson, M. I. Tenaillon, B. S. Gaut, and E. S. Buckler IV. 2002. Genetic diversity and selction in the maize starch pathway. Proc. Natl. Acad. Sci. U.S.A. 99:12959-12962.
64. Zhang, L., A. S. Peek, D. Dunams, and B. S. Gaut. 2002a. Population genetics of duplicated disease defense genes, hm1 and hm2, in maize (Zea mays ssp. mays L.) and its wild ancestor (Zea mays ssp. parviglumis). Genetics 162:851-860.
65. Zhang, L., T. J. Vision, and B. S. Gaut. 2002b. Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana. Mol. Biol. Evol. 19:1464-1473.